Topological connectivity analysis of accumulated radiation damage from multiple molecular dynamics recoil cascades

2012 ◽  
Vol 1475 ◽  
Author(s):  
Henry R. Foxhall ◽  
John H. Harding ◽  
Karl P. Travis
Keyword(s):  
Molecular Dynamics ◽  
Kinetic Energy ◽  
Radiation Damage ◽  
Large Scale ◽  
Structural Evolution ◽  
Md Simulations ◽  
Recoil Atom ◽  
Connectivity Analysis ◽  
Topological Connectivity ◽  
Insight Into

ABSTRACTThe results of sequential large-scale molecular dynamics (MD) simulations of radiation damage cascades in Gd2Ti2O7 and Gd2Zr2O7 are presented. Twelve alpha recoil cascades, each due to a recoil atom with 40 keV of kinetic energy, are performed in both materials and a stark contrast in behaviour observed. Topological connectivity analysis is used to analyse the structural evolution of the two systems. Our results provide important insight into accumulation of disorder in pyrochlore-structured ceramics.

scholarly journals KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability

2021 ◽  
Vol 22 (10) ◽  
pp. 5408
Author(s):  
Carter Wilson ◽  
Megan Chang ◽  
Mikko Karttunen ◽  
Wing-Yiu Choy
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Md Simulations ◽  
Covalent Modification ◽  
Additional Insight ◽  
New Class ◽  
Kelch Domain ◽  
Cancer Mutations ◽  
Mutagenic Effects ◽  
Insight Into

We have performed 280 μs of unbiased molecular dynamics (MD) simulations to investigate the effects of 12 different cancer mutations on Kelch-like ECH-associated protein 1 (KEAP1) (G333C, G350S, G364C, G379D, R413L, R415G, A427V, G430C, R470C, R470H, R470S and G476R), one of the frequently mutated proteins in lung cancer. The aim was to provide structural insight into the effects of these mutants, including a new class of ANCHOR (additionally NRF2-complexed hypomorph) mutant variants. Our work provides additional insight into the structural dynamics of mutants that could not be analyzed experimentally, painting a more complete picture of their mutagenic effects. Notably, blade-wise analysis of the Kelch domain points to stability as a possible target of cancer in KEAP1. Interestingly, structural analysis of the R470C ANCHOR mutant, the most prevalent missense mutation in KEAP1, revealed no significant change in structural stability or NRF2 binding site dynamics, possibly indicating an covalent modification as this mutant’s mode of action.

scholarly journals Large-Scale Molecular Dynamics Simulations of Homogeneous Nucleation of Pure Aluminium

Metals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 1217 ◽  
Author(s):  
Papanikolaou ◽  
Salonitis ◽  
Jolly ◽  
Frank
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Solidification Process ◽  
Md Simulations ◽  
Pure Aluminium ◽  
3 Dimensional ◽  
Hexagonal Close Packed ◽  
Simulation Domain ◽  
Dynamics Simulations ◽  
Insight Into

Despite the continuous and remarkable development of experimental techniques for the investigation of microstructures and the growth of nuclei during the solidification of metals, there are still unknown territories around this topic. The solidification in nanoscale can be effectively investigated by means of molecular dynamics (MD) simulations which can provide a deep insight into the mechanisms of the formation of nuclei and the induced crystal structures. In this study, MD simulations were performed to investigate the solidification of pure Aluminium and the effects of the cooling rate on the final properties of the solidified material. A large number of Aluminium atoms were used in order to investigate the grain growth over time and the formation of stacking faults during solidification. The number of face-centred cubic (FCC), hexagonal close-packed (HCP) and body-centred cubic (BCC) was recorded during the evolution of the process to illustrate the nanoscale mechanisms initiating solidification. The current investigation also focuses on the exothermic nature of the solidification process which has been effectively captured by means of MD simulations using 3 dimensional representations of the kinetic energy across the simulation domain.

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

scholarly journals Antimicrobial action of the cationic peptide, chrysophsin-3: a coarse-grained molecular dynamics study

Soft Matter ◽  
2018 ◽  
Vol 14 (15) ◽  
pp. 2796-2807 ◽  
Author(s):  
Andrea Catte ◽  
Mark R. Wilson ◽  
Martin Walker ◽  
Vasily S. Oganesyan
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Md Simulations ◽  
Antimicrobial Action ◽  
Coarse Grained ◽  
Cationic Peptide ◽  
Coarse Grained Molecular Dynamics

Antimicrobial action of a cationic peptide is modelled by large scale MD simulations.

scholarly journals Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when

2019 ◽  
Author(s):  
Juan J Galano-Frutos ◽  
Helena García-Cebollada ◽  
Javier Sancho
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Large Scale ◽  
Binary Classification ◽  
Chemical Properties ◽  
Md Simulations ◽  
Single Amino Acid ◽  
Medical Decision ◽  
Evolutionary Information ◽  
Protein Variants

Abstract The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical–chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80–85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore’s law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants.

scholarly journals Hydrogenation Dynamics of Biphenylene Carbon (Graphenylene) Membranes

MRS Advances ◽  
2017 ◽  
Vol 2 (29) ◽  
pp. 1571-1576
Author(s):  
Vinicius Splugues ◽  
Pedro Alves da Silva Autreto ◽  
Douglas S. Galvao
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Md Simulations ◽  
Structural Transformations ◽  
Extensive Study ◽  
Massively Parallel ◽  
Porous Membranes ◽  
Two Dimensional ◽  
Reactive Force

ABSTRACTThe advent of graphene created a revolution in materials science. Because of this there is a renewed interest in other carbon-based structures. Graphene is the ultimate (just one atom thick) membrane. It has been proposed that graphene can work as impermeable membrane to standard gases, such argon and helium. Graphene-like porous membranes, but presenting larger porosity and potential selectivity would have many technological applications. Biphenylene carbon (BPC), sometimes called graphenylene, is one of these structures. BPC is a porous two-dimensional (planar) allotrope carbon, with its pores resembling typical sieve cavities and/or some kind of zeolites. In this work, we have investigated the hydrogenation dynamics of BPC membranes under different conditions (hydrogenation plasma density, temperature, etc.). We have carried out an extensive study through fully atomistic molecular dynamics (MD) simulations using the reactive force field ReaxFF, as implemented in the well-known Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. Our results show that the BPC hydrogenation processes exhibit very complex patterns and the formation of correlated domains (hydrogenated islands) observed in the case of graphene hydrogenation was also observed here. MD results also show that under hydrogenation BPC structure undergoes a change in its topology, the pores undergoing structural transformations and extensive hydrogenation can produce significant structural damages, with the formation of large defective areas and large structural holes, leading to structural collapse.

scholarly journals Indentation-induced plastic behaviour of nanotwinned Cu/high entropy alloy FeCoCrNi nanolaminate: an atomic simulation

RSC Advances ◽  
2020 ◽  
Vol 10 (16) ◽  
pp. 9187-9192 ◽  
Author(s):  
Hui Feng ◽  
Jingwen Tang ◽  
Haotian Chen ◽  
Yuanyuan Tian ◽  
Qihong Fang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Md Simulations ◽  
High Entropy Alloy ◽  
High Entropy ◽  
Atomic Simulation ◽  
Layer Number ◽  
Plastic Behaviour

Using large-scale molecular dynamics (MD) simulations, the effects of interface and layer number in the nanoindentation response of experimentally observed nanotwinned Cu/high entropy alloy (HEA) FeCoCrNi nanolaminate are studied.

Nanomechanical and Friction Properties of Ultrathin Amorphous Carbon Films Studied by Molecular Dynamics Analysis

2010 ◽  
Author(s):  
N. Wang ◽  
K. Komvopoulos
Keyword(s):  
Molecular Dynamics ◽  
Amorphous Carbon ◽  
Md Simulations ◽  
Carbon Films ◽  
Magnetic Storage ◽  
Disk Drives ◽  
Magnetic Medium ◽  
High Density Magnetic Recording ◽  
Protective Overcoats ◽  
Insight Into

An ultrathin (<4 nm) film of amorphous carbon (a-C) is used in contemporary disk drives to protect the magnetic medium of the hard disk from corrosion and mechanical wear due to intermittent impact of the low-flying magnetic head. Because of increasing demands for much higher magnetic storage densities (i.e., >10 Tbits/in2), the a-C film thickness must be decreased to <2 nm. However, the tribological and mechanical properties of such thin a-C films are not well understood and, moreover, are extremely difficult to determine experimentally. The objective of this study was to obtain insight into the tribological behavior of ultrathin a-C films by performing molecular dynamics (MD) simulations. MD results of the hardness and friction properties of nanometer-thick a-C films are interpreted in terms of the ratio of tetrahedral-to-trigonal carbon atom hybridization. A critical thickness for the effective protection of the magnetic medium by the a-C film is estimated from MD results. The results of this study elucidate the nanomechanical and nanotribological properties of ultrathin a-C films used as protective overcoats in extremely-high-density magnetic recording.

MOLECULAR-DYNAMICS SIMULATION OF RADIATION DAMAGE ON COPPER CLUSTERS

2000 ◽  
Vol 11 (05) ◽  
pp. 1025-1032
Author(s):  
ŞAKIR ERKOÇ
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Kinetic Energy ◽  
Potential Energy ◽  
Radiation Damage ◽  
Potential Energy Function ◽  
Dynamics Simulation ◽  
External Radiation ◽  
Empirical Potential ◽  
Copper Clusters

The effect of radiation damage on copper clusters has been investigated by performing molecular-dynamics simulation using empirical potential energy function for interaction between copper atoms. The external radiation is modeled by giving extra kinetic energy in the range of 5–50 eV to initially chosen atom in the cluster. It has been found that the atom having extra kinetic energy dissociates independently from the amount of given energy in the studied range.

scholarly journals A Virtual Reality Ensemble Molecular Dynamics Workflow to Study Complex Conformational Changes in Proteins

2020 ◽  
Author(s):  
Jordi Juárez-Jiménez ◽  
Philip Tew ◽  
Michael o'connor ◽  
Salome Llabres ◽  
Rebecca Sage ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Virtual Reality ◽  
Conformational Changes ◽  
Large Scale ◽  
A Priori ◽  
Computational Cost ◽  
Md Simulations ◽  
Collective Variables ◽  
Sampling Protocols ◽  
State Models

<p>Molecular dynamics (MD) simulations are increasingly used to elucidate relationships between protein structure, dynamics and their biological function. Currently it is extremely challenging to perform MD simulations of large-scale structural rearrangements in proteins that occur on millisecond timescales or beyond, as this requires very significant computational resources, or the use of cumbersome ‘collective variable’ enhanced sampling protocols. Here we describe a framework that combines ensemble MD simulations and virtual-reality visualization (eMD-VR) to enable users to interactively generate realistic descriptions of large amplitude, millisecond timescale protein conformational changes in proteins. Detailed tests demonstrate that eMD-VR substantially decreases the computational cost of folding simulations of a WW domain, without the need to define collective variables <i>a priori</i>. We further show that eMD-VR generated pathways can be combined with Markov State Models to describe the thermodynamics and kinetics of large-scale loop motions in the enzyme cyclophilin A. Our results suggest eMD-VR is a powerful tool for exploring protein energy landscapes in bioengineering efforts. </p>

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